LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-930-g7036930360)
# pour particles into cone-shaped funnel, settle them, let them run out bottom

variable	name string funnel_pour

thermo_modify	flush yes
units 		si
variable	PI equal 3.141592653589
variable	seed equal 14314

###############################################
# Geometry-related parameters
###############################################

variable	xlo equal 10
variable	xhi equal 40
variable	ylo equal 10
variable	yhi equal 40
variable	zlo equal -20
variable	zhi equal 50

variable	xc equal 25
variable	yc equal 25

variable	zconehi equal 50
variable	zconelo equal 10
variable	zcyllo equal 0
variable	radconelo equal 2
variable	radconehi equal 20

################################################
# Particle sizes
################################################

variable	rlo equal 0.25
variable	rhi equal 0.5
variable	dlo equal 2.0*${rlo}
variable	dlo equal 2.0*0.25
variable	dhi equal 2.0*${rhi}
variable	dhi equal 2.0*0.5

variable 	skin equal ${rhi}
variable 	skin equal 0.5

###############################################
# Granular contact parameters
###############################################

variable	coeffRes equal 0.1
variable	coeffFric equal 0.5

variable	density equal 1.0
variable	EYoung equal 10^5
variable 	Poisson equal 2.0/7.0
variable	GShear equal ${EYoung}/(2*(1+${Poisson}))
variable	GShear equal 100000/(2*(1+${Poisson}))
variable	GShear equal 100000/(2*(1+0.285714285714286))

variable	gravity equal 1.0

variable	reff equal 0.5*(${rhi}+${rlo})
variable	reff equal 0.5*(0.5+${rlo})
variable	reff equal 0.5*(0.5+0.25)
variable	meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable	meff equal 1*4.0/3.0*${PI}*${reff}^3
variable	meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable	meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable	min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable	min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable	max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable	max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5

## Typical way to set kn, kt, etc.:
variable        kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable        kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable        kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable        kt equal 4.0*${GShear}/(2-${Poisson})
variable        kt equal 4.0*38888.8888888889/(2-${Poisson})
variable        kt equal 4.0*38888.8888888889/(2-0.285714285714286)

variable	a equal (-2.0*log(${coeffRes})/${PI})^2
variable	a equal (-2.0*log(0.1)/${PI})^2
variable	a equal (-2.0*log(0.1)/3.141592653589)^2
variable        gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable        gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable        gamma_t equal ${gamma_n}*0.5
variable        gamma_t equal 903.503751814138*0.5

variable	tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable	tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)

variable	dt equal ${tcol}*0.05
variable	dt equal 0.00210943016014969*0.05
timestep	${dt}
timestep	0.000105471508007485

###############################################
variable	dumpfreq equal 1000
variable	logfreq equal 1000

newton 		off
atom_style	sphere

boundary	p p f

region		boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region		boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region		boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region		boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region		boxreg block 10 40 10 40 ${zlo} ${zhi}
region		boxreg block 10 40 10 40 -20 ${zhi}
region		boxreg block 10 40 10 40 -20 50
create_box	1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
  1 by 1 by 4 MPI processor grid

pair_style	gran/hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style	gran/hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff	* *

neighbor        ${skin} multi
neighbor        0.5 multi
thermo 		${logfreq}
thermo 		1000

comm_style	brick
comm_modify 	mode multi group all vel yes
balance		1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 0
  ghost atom cutoff = 0
  binsize = 30, bins = 1 1 3
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair gran/hertz/history, perpetual
      attributes: half, newton off, size, history
      pair build: half/size/multi/atomonly/newtoff
      stencil: full/multi/3d
      bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
fix		bal all balance 10000 1.1 shift xyz 20 1.01

####################### Options specific to pouring #########################

# insertion region for fix/pour

region	     	insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region	     	insreg cylinder z 25 ${yc} 10 30 50 side in units box
region	     	insreg cylinder z 25 25 10 30 50 side in units box

# define cone and cylinder regions - see lammps doc on region command
# note new open options

region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 #Top is open
region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 2 
region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 2 

region		conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 #Bottom and top are open
region		conereg cone z 25 ${yc} ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 ${radconelo} ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 ${radconehi} 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 20 		${zconelo} ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 20 		10 ${zconehi} side in units box 		open 1 open 2 
region		conereg cone z 25 25 2 20 		10 50 side in units box 		open 1 open 2 

region		hopreg union 2 conereg cylreg

fix		grav all gravity ${gravity} vector 0 0 -1
fix		grav all gravity 1 vector 0 0 -1
fix		1 all nve/sphere


fix		hopper3 all wall/gran/region hertz/history                 ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history                 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg

fix		ins all pour 2000 1 42424 region insreg 		diam range ${dlo} ${dhi} dens ${density} ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 ${dhi} dens ${density} ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens ${density} ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 ${density}
fix		ins all pour 2000 1 42424 region insreg 		diam range 0.5 1 dens 1 1

#dump		1 all custom ${dumpfreq} ${name}.dump #		id type mass diameter x y z

#dump		2 all image 4000 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30 zoom 3.0 #                box no 0.0 axes no 0.0 0.0
#dump_modify	2 pad 6

thermo_style	custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:904)
thermo_modify	flush yes lost warn

# Initial run to fill up the cone

run		20000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Particle insertion: 3000 every 59965 steps, 2000 by step 1
Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
   Step          CPU          Atoms        KinEng    
         0   0                      0  -0            
      1000   0.44807882          2000  -0            
      2000   0.63550417          2000  -0            
      3000   0.82082211          2000  -0            
      4000   1.0004254           2000  -0            
      5000   1.1738611           2000  -0            
      6000   1.3426033           2000  -0            
      7000   1.5076494           2000  -0            
      8000   1.6673766           2000  -0            
      9000   1.8244007           2000  -0            
     10000   1.9794011           2000  -0            
     11000   2.049584            2000  -0            
     12000   2.1210622           2000  -0            
     13000   2.1917604           2000  -0            
     14000   2.2631006           2000  -0            
     15000   2.3361511           2000  -0            
     16000   2.4131306           2000  -0            
     17000   2.4938482           2000  -0            
     18000   2.5771299           2000  -0            
     19000   2.6633207           2000  -0            
     20000   2.7541527           2000  -0            
Loop time of 2.75417 on 4 procs for 20000 steps with 2000 atoms

99.5% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.028725   | 0.079701   | 0.18206    |  21.3 |  2.89
Neigh   | 0.0072627  | 0.013673   | 0.023071   |   5.0 |  0.50
Comm    | 0.084562   | 0.18785    | 0.28115    |  18.6 |  6.82
Output  | 0.00088257 | 0.0016453  | 0.0021961  |   1.2 |  0.06
Modify  | 0.66551    | 1.1062     | 1.9324     |  46.7 | 40.16
Other   |            | 1.365      |            |       | 49.57

Nlocal:            500 ave         510 max         493 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost:            154 ave         227 max          79 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs:          415.5 ave         610 max         258 min
Histogram: 1 1 0 0 0 0 1 0 0 1

Total # of neighbors = 1662
Ave neighs/atom = 0.831
Neighbor list builds = 71
Dangerous builds = 0
unfix 		ins
run		150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
   Step          CPU          Atoms        KinEng    
     20000   0                   2000   6652.2957    
     21000   0.064679537         2000   6807.2201    
     22000   0.13180546          2000   6973.9359    
     23000   0.20116485          2000   7142.3648    
     24000   0.27404997          2000   7276.9717    
     25000   0.35093997          2000   7369.4191    
     26000   0.43258785          2000   7497.6526    
     27000   0.51758599          2000   7638.946     
     28000   0.60693744          2000   7780.0339    
     29000   0.7014587           2000   7881.8177    
     30000   0.80119592          2000   7967.2641    
     31000   0.87335402          2000   7994.9273    
     32000   0.95320537          2000   7937.0672    
     33000   1.0398918           2000   7774.0508    
     34000   1.1351184           2000   7591.1511    
     35000   1.2382665           2000   7357.5032    
     36000   1.3492928           2000   7147.3776    
     37000   1.467685            2000   6980.0719    
     38000   1.5926331           2000   6813.0872    
     39000   1.7265338           2000   6657.0693    
     40000   1.8700751           2000   6505.1155    
     41000   1.9833133           2000   6330.2864    
     42000   2.1004898           2000   6147.8022    
     43000   2.2208699           2000   5932.9244    
     44000   2.3442041           2000   5755.296     
     45000   2.4697527           2000   5511.622     
     46000   2.6055398           2000   5332.3171    
     47000   2.7455054           2000   5162.4926    
     48000   2.8851384           2000   5044.5764    
     49000   3.0239861           2000   4901.1141    
     50000   3.1614979           2000   4731.1949    
     51000   3.2810383           2000   4575.418     
     52000   3.4070575           2000   4428.9425    
     53000   3.5378444           2000   4291.7282    
     54000   3.6714875           2000   4154.1885    
     55000   3.8108149           2000   3994.9402    
     56000   3.9546982           2000   3855.5977    
     57000   4.0997167           2000   3672.9504    
     58000   4.2491708           2000   3435.3395    
     59000   4.408196            2000   3200.7379    
     60000   4.5700117           2000   2986.5411    
     61000   4.723306            2000   2747.3628    
     62000   4.878128            2000   2542.0805    
     63000   5.0341944           2000   2336.7687    
     64000   5.1923913           2000   2151.6388    
     65000   5.3556896           2000   1933.6773    
     66000   5.5238885           2000   1699.0747    
     67000   5.6948336           2000   1467.7209    
     68000   5.8690421           2000   1227.3577    
     69000   6.0509636           2000   1016.2766    
     70000   6.2387022           2000   812.90843    
     71000   6.4073364           2000   632.88108    
     72000   6.577617            2000   470.67731    
     73000   6.7470437           2000   360.47748    
     74000   6.9135965           2000   286.10584    
     75000   7.0795553           2000   229.70386    
     76000   7.2433614           2000   179.62654    
     77000   7.4108991           2000   142.40417    
     78000   7.5787629           2000   113.55745    
     79000   7.7455158           2000   93.787669    
     80000   7.9119881           2000   80.646319    
     81000   8.0788298           2000   70.944319    
     82000   8.2481597           2000   59.2275      
     83000   8.4164166           2000   49.633808    
     84000   8.5904585           2000   42.882698    
     85000   8.768017            2000   36.841824    
     86000   8.9516342           2000   31.776681    
     87000   9.1361653           2000   28.25076     
     88000   9.3230302           2000   25.228966    
     89000   9.5111334           2000   22.593627    
     90000   9.7013966           2000   21.15796     
     91000   9.8899455           2000   19.941629    
     92000   10.082329           2000   18.375654    
     93000   10.276769           2000   17.056701    
     94000   10.474742           2000   16.192511    
     95000   10.674727           2000   15.572922    
     96000   10.874807           2000   14.827788    
     97000   11.075291           2000   13.919613    
     98000   11.275072           2000   13.19525     
     99000   11.475537           2000   11.993376    
    100000   11.677999           2000   11.258787    
    101000   11.88024            2000   10.641688    
    102000   12.084353           2000   10.430435    
    103000   12.288658           2000   9.518069     
    104000   12.4935             2000   9.1332086    
    105000   12.70028            2000   9.2151611    
    106000   12.908347           2000   9.0035132    
    107000   13.116082           2000   8.7835861    
    108000   13.324126           2000   8.5124479    
    109000   13.53208            2000   8.2975453    
    110000   13.740687           2000   8.3483043    
    111000   13.948107           2000   8.4658572    
    112000   14.156079           2000   8.4771784    
    113000   14.364341           2000   7.8937975    
    114000   14.574123           2000   7.2472953    
    115000   14.783651           2000   6.5812074    
    116000   14.99421            2000   5.5651566    
    117000   15.204441           2000   5.3015807    
    118000   15.415336           2000   5.0133941    
    119000   15.625609           2000   4.8746036    
    120000   15.836675           2000   4.9133073    
    121000   16.047261           2000   4.3337392    
    122000   16.257951           2000   4.3374836    
    123000   16.468869           2000   4.3721818    
    124000   16.680533           2000   4.3894508    
    125000   16.890783           2000   4.1811774    
    126000   17.103698           2000   4.3011002    
    127000   17.315003           2000   4.442228     
    128000   17.526696           2000   4.6170394    
    129000   17.738415           2000   4.8184318    
    130000   17.952565           2000   4.8442096    
    131000   18.165389           2000   4.9668117    
    132000   18.378094           2000   4.8364562    
    133000   18.592482           2000   4.6658645    
    134000   18.804443           2000   4.5758487    
    135000   19.016578           2000   4.7251949    
    136000   19.230118           2000   4.5846492    
    137000   19.443202           2000   4.7565986    
    138000   19.656431           2000   4.8186623    
    139000   19.867627           2000   4.6571647    
    140000   20.080227           2000   4.0730143    
    141000   20.292696           2000   4.0605542    
    142000   20.503397           2000   4.1457179    
    143000   20.714516           2000   4.3418042    
    144000   20.925902           2000   4.0323813    
    145000   21.139161           2000   3.8064958    
    146000   21.352466           2000   3.1802044    
    147000   21.564201           2000   2.7947641    
    148000   21.772853           2000   2.7384164    
    149000   21.983847           2000   2.7428829    
    150000   22.196524           2000   2.7802186    
    151000   22.408229           2000   2.6703451    
    152000   22.619074           2000   2.3357647    
    153000   22.829739           2000   1.9855305    
    154000   23.039835           2000   1.9442713    
    155000   23.252204           2000   1.7348027    
    156000   23.464375           2000   1.5699942    
    157000   23.677869           2000   1.5224944    
    158000   23.888064           2000   1.4850914    
    159000   24.099703           2000   1.4461048    
    160000   24.312523           2000   1.3759525    
    161000   24.522295           2000   0.83754463   
    162000   24.733904           2000   0.7952922    
    163000   24.944962           2000   0.69670143   
    164000   25.155399           2000   0.66253723   
    165000   25.36618            2000   0.64602969   
    166000   25.576713           2000   0.60229858   
    167000   25.788559           2000   0.5757589    
    168000   25.998455           2000   0.5996023    
    169000   26.209944           2000   0.62130448   
    170000   26.420855           2000   0.63888277   
Loop time of 26.4209 on 4 procs for 150000 steps with 2000 atoms

97.0% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.6691     | 8.9481     | 11.368     |  85.5 | 33.87
Neigh   | 0.087705   | 0.14369    | 0.18343    |   9.2 |  0.54
Comm    | 1.9172     | 3.5612     | 4.2565     |  50.7 | 13.48
Output  | 0.0045151  | 0.0090615  | 0.016477   |   4.7 |  0.03
Modify  | 5.4247     | 7.6604     | 9.1464     |  49.8 | 28.99
Other   |            | 6.099      |            |       | 23.08

Nlocal:            500 ave         538 max         419 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost:          445.5 ave         688 max         200 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs:        4500.25 ave        5610 max        3443 min
Histogram: 1 0 1 0 0 0 1 0 0 1

Total # of neighbors = 18001
Ave neighs/atom = 9.0005
Neighbor list builds = 362
Dangerous builds = 0

# remove "plug" - need to redefine cylinder region & union

region	  	cylreg delete
region		hopreg delete
region	    	cylreg cylinder z ${xc} ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 #Bottom & top are open
region	    	cylreg cylinder z 25 ${yc} ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 ${radconelo} 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 2 		${zcyllo} ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 2 		0 ${zconelo} side in units box 		open 1 open 2 
region	    	cylreg cylinder z 25 25 2 		0 10 side in units box 		open 1 open 2 

region		hopreg union 2 cylreg conereg

unfix		hopper3
fix		hopper3 all wall/gran/region hertz/history 		${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix		hopper3 all wall/gran/region hertz/history 		72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg

run		100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
   Step          CPU          Atoms        KinEng    
    170000   0                   2000   0.63888277   
    171000   0.21222344          2000   1.4139245    
    172000   0.42521156          2000   2.2400138    
    173000   0.63924412          2000   3.8034979    
    174000   0.85157975          2000   6.116727     
    175000   1.065247            2000   8.9536458    
    176000   1.2785495           2000   12.74348     
    177000   1.4916668           2000   17.410816    
    178000   1.7042214           2000   22.879174    
    179000   1.9186225           2000   28.966022    
    180000   2.1345716           2000   35.449239    
    181000   2.3486488           2000   42.694882    
    182000   2.5624316           2000   50.913279    
    183000   2.7760261           2000   60.098465    
    184000   2.9883219           2000   70.133474    
    185000   3.2007559           2000   80.950013    
    186000   3.4107595           2000   92.495525    
    187000   3.6204368           2000   104.83034    
    188000   3.8298085           2000   118.04659    
    189000   4.0383423           2000   132.7403     
    190000   4.2477798           2000   148.31955    
    191000   4.4421194           2000   164.26321    
    192000   4.6373112           2000   180.6933     
    193000   4.829991            2000   197.72012    
    194000   5.02323             2000   215.43637    
    195000   5.2162947           2000   234.29738    
    196000   5.4075928           2000   254.03407    
    197000   5.5974162           2000   274.58626    
    198000   5.7869821           2000   296.88915    
    199000   5.976701            2000   320.45001    
    200000   6.1650648           2000   344.75891    
    201000   6.3509022           2000   370.14016    
    202000   6.5363704           2000   395.72827    
    203000   6.7222457           2000   420.42026    
    204000   6.9107246           2000   446.08079    
    205000   7.0996055           2000   473.62963    
    206000   7.2878276           2000   501.05693    
    207000   7.4753237           2000   530.40427    
    208000   7.6643827           2000   560.62015    
    209000   7.8553563           2000   593.00113    
    210000   8.0454619           2000   626.36661    
    211000   8.2342734           2000   661.34861    
    212000   8.4248464           2000   697.41001    
    213000   8.6166264           2000   735.12299    
    214000   8.8061303           2000   773.89126    
    215000   8.9932827           2000   813.83268    
    216000   9.1797117           2000   854.63669    
    217000   9.3642361           2000   896.59089    
    218000   9.5486397           2000   938.70251    
    219000   9.7300675           2000   982.10773    
    220000   9.9142511           2000   1025.2953    
    221000   10.098593           2000   1069.8382    
    222000   10.284654           2000   1115.4449    
    223000   10.47145            2000   1161.6742    
    224000   10.656994           2000   1211.289     
    225000   10.839264           2000   1262.8074    
    226000   11.019273           2000   1316.6353    
    227000   11.198463           2000   1370.7434    
WARNING: Lost atoms: original 2000 current 1991 (../thermo.cpp:499)
    228000   11.377846           1991   1382.0924    
    229000   11.557302           1986   1407.1543    
    230000   11.737106           1975   1415.708     
    231000   11.915389           1968   1430.6498    
    232000   12.095672           1957   1421.0352    
    233000   12.275267           1939   1376.0322    
    234000   12.452526           1925   1350.1292    
    235000   12.629207           1912   1337.0529    
    236000   12.80204            1893   1273.2219    
    237000   12.975817           1879   1207.0473    
    238000   13.152228           1861   1132.0109    
    239000   13.331267           1846   1083.1042    
    240000   13.510046           1826   1004.3265    
    241000   13.67647            1819   989.36186    
    242000   13.842216           1812   983.26132    
    243000   14.006163           1805   985.79932    
    244000   14.168208           1794   936.34844    
    245000   14.331979           1784   889.17423    
    246000   14.495868           1770   846.65018    
    247000   14.662081           1753   751.16306    
    248000   14.830163           1740   709.23095    
    249000   14.999432           1732   687.61586    
    250000   15.166285           1721   638.82967    
    251000   15.331363           1714   618.71543    
    252000   15.493524           1709   611.25444    
    253000   15.651829           1705   606.6846     
    254000   15.809586           1702   601.7236     
    255000   15.966097           1697   575.97244    
    256000   16.12731            1695   577.1712     
    257000   16.292272           1691   576.93668    
    258000   16.460463           1688   586.63687    
    259000   16.628863           1686   581.52487    
    260000   16.797813           1682   566.49544    
    261000   16.95041            1681   586.18628    
    262000   17.101549           1678   582.11927    
    263000   17.251379           1675   589.96041    
    264000   17.403824           1672   577.55581    
    265000   17.556094           1669   570.45998    
    266000   17.710318           1666   574.0576     
    267000   17.865801           1662   578.07385    
    268000   18.019798           1660   587.65705    
    269000   18.177178           1657   584.43358    
    270000   18.332227           1654   591.22601    
Loop time of 18.3323 on 4 procs for 100000 steps with 1654 atoms

96.2% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.7775     | 6.3596     | 9.2369     |  92.3 | 34.69
Neigh   | 0.088842   | 0.10453    | 0.12331    |   4.2 |  0.57
Comm    | 1.1938     | 2.7006     | 3.3247     |  53.6 | 14.73
Output  | 0.0013814  | 0.0063655  | 0.013334   |   5.5 |  0.03
Modify  | 4.3454     | 4.8952     | 5.3813     |  20.7 | 26.70
Other   |            | 4.266      |            |       | 23.27

Nlocal:          413.5 ave         429 max         408 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost:         408.25 ave         653 max         182 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:        3486.25 ave        4367 max        2213 min
Histogram: 1 0 0 0 0 1 0 0 1 1

Total # of neighbors = 13945
Ave neighs/atom = 8.4310762
Neighbor list builds = 227
Dangerous builds = 0
Total wall time: 0:00:47
